Chancellor Rudy Crew’s top aides yesterday threatened to join their boss in quitting over school vouchers – even as Mayor Giuliani tried to cool tempers by saying he doubts Crew will resign.

“Let’s stop the threat stuff. This isn’t about quitting. This is an idea, this is a thought,” said Giuliani during his monthly call-in show last night on WCBS radio.

“I think that this discussion can go on, it can be debated. I don’t think the chancellor is going to quit over a discussion of an idea like this.”

Crew dropped a bombshell Wednesday when he said he would resign if Giuliani presses ahead with plans to spend $12 million on a voucher program to give kids in one city district tuition to go to private schools.

Giuliani supports vouchers because they give poor parents the same opportunity as rich parents to send their children to private schools and would create competition that could improve public education.

There were no signs of cooling off from Board of Education headquarters. Crew’s return from a speaking engagement in California was postponed by an ear infection, and he was unavailable for comment.

But his top aides were adamant about his stand on vouchers.

“If the chancellor leaves, I’m leaving and there will be a number of people who will also leave immediately,” said Deputy Chancellor Harry Spence.

Giuliani and Crew have been the closest of allies. After Gov. Pataki appointed a commission last month to investigate the city’s schools, Giuliani sprang to Crew’s defense, repeatedly calling him one of the best chancellors the city has ever had.

Spence said the mayor’s campaign for vouchers pushed Crew over the edge.

“There have been issues resolved before, but this one is different. It hits the heart of what the chancellor believes in,” Spence said.

He predicted the battle over vouchers “will play out rather quickly. A decision will have to be made soon.”

He said the proposal to create vouchers would likely come up for a vote at the school board’s meeting next week. Six of the board’s seven members are split over the voucher plan, with only Terri Thomson of Queens still undecided.

Giuliani met yesterday with Thomson and the woman who appointed her, Queens Borough President Claire Shulman.

Shulman’s spokesman, Dan Andrews, said the mayor and borough president appeared willing to negotiate the voucher issue, describing the talks as a “very good discussion.”

“They agreed to examine other options,” Andrews said. But he went on to add, cryptically, that “vouchers are not off the table.”

“The only reason he would have done this is because of his deep-seated view about this issue,” said Weingarten.

Crew’s threat left a host of city and state officials bewildered because they say vouchers would never get the legislative approval needed here or in Albany.

“For the chancellor to throw himself on the sword over the voucher program may be grossly premature since we have no willingness to go ahead with it,” said City Councilman Herb Berman, (D-Brooklyn), chairman of the Finance Committee.

State Education Commissioner Richard Mills said state laws bar the use of tax dollars for private tuition.